Bioinformatics

Sequence only

• Servers and programs for sequence analysis

Sequence to structure

• Prediction of structure from sequence: servers and programs
• Mapping sequence alignment to a structure

Structure to Sequence

• Structure based sequence alignment
• structural motifs in the PDB

Structure only

• Ligand display
• Servers for ligand topologies/parameters
• Servers and programs for protein structure analysis
• Programs for nucleic acid structure analysis
• Morphing and making movies
• Programs for representing the surface of a channel inside protein
• database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam
• Rosetta Alanine Scanning each residue in a interface is mutated to Ala; local minimisation is performed, and the binding energy is calculated
• solvent-accessible surface
• topology plots

Structural superposition

has its own article.

Domain definition

• http://pdomains.sdsc.edu offering an interface for comparing a number of different methods for automatic domain definition. For domain interfaces SCOPPI may be helpful.
• http://www.ebi.ac.uk/pdbe/docs/sifts/ a list of tab delimited files that contain all the information for each chain in the PDB. The information is also available per residue in XML format that contain additional annotation. These files are updated every week.
• A collection of links to structure-based domain parsers is at http://binf.gmu.edu/ttaylor/homepagelinks.html
• Domain boundaries are available through RCSB PDB RESTful web services described at: http://www.pdb.org/pdb/software/rest.do. For example, the URL http://www.pdb.org/pdb/rest/das/pdbchainfeatures/features?segment=1AJH.A returns an XML file with SCOP, CATH, DP, PDP, PFAM, InterPro domain boundaries, plus secondary structure information by DSSP, STRIDE, and the structure author.
• In the sequence tab for each PDB entry, (for example, http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=1AJH), the domain assignment from SCOP, DP, CATH etc. are given.

Functional annotation

• GOdot webserver for predicting function from structure (see http://dx.plos.org/10.1371%2Fjournal.pcbi.1000105)
• ProFunc Analysis of a protein's 3D structure to help identify its likely biochemical function
• Annotation PSI Stuctural Genomics knowledgebase

Docking

• ClusPro - easy to use web interface
• Rosetta can do much more than just docking, but is difficult to use
• 3D-dock - uses an algorithm that mainly looks at surface complimentarity between the two proteins
• Dave Ritchie's Hex program - it is blisteringly quick
• Haddock - recommended by Tassos
• AutoDock - Wiki at https://www.nbcr.net/pub/wiki/index.php?title=AutoDock
• DockBlaster - runs DOCK 3.5.54; there's a wiki
• SymmDock

Hydrophobic patches

1. https://sbgrid.org/software/titles/quilt
2. Swiss PDBViewer, detect hydrophobic patches under Tool Surface
3. EBI PISA and look for negative delta G
4. look at protein-protein interaction and interface dbases
5. Waltz is an excellent web-server to give very good results on amyloidogenic regions based on sequence stretches (correlate the regions with hydrophobic patches by hydropathy plot obtained from Expasy-Protscale).
6. Aggrescan
7. Aggrescan's 3D counterpart http://biocomp.chem.uw.edu.pl/A3D/ - It even allows you to consider whether structures reached by coarse-grained MD are more aggregation-prone than your starting structure.
8. PASTA
9. with pdb structure you can use the Maestro program (from Schrodinger Inc.)

Other stuff

• pKa of protein - evaluated in: Crystallography Reviews, Volume 15, Issue 4 October 2009 , pages 231 - 259 An evaluation review of the prediction of protonation states in proteins versus crystallographic experiment Authors: Stuart J. Fisher; James Wilkinson; Richard H. Henchman; John R. Helliwell available at:- http://www.informaworld.com/smpp/content~db=all~content=a915050320~tab=content~order=page
• Programs for visualization (see also Model building)
• Links to Bioinformatics websites
• programs with chemistry knowledge, e.g. to build 3D-coordinates from 2D drawings
• modeling of glycosylation with GlyProt
• PDBeStatistics and some explanation of it